Previously it was shown that a low molecular mass fraction isolated from the proteose–peptone preparation of milk, fraction E, inhibited milk coagulation. Here, the composition and molecular mass of fraction E, and its effect on milk clotting parameters, was investigated to better understand its mechanism of action. Fraction E comprised casein-derived peptides of 1–3 kDa rich in phosphorus residues. Fraction E content increased substantially in milk from glands infected with Escherichia coli and Streptococcus dysgalactiae, and during storage of the milk. However, the specific activity of fraction E on milk clotting parameters was the same whether sampled from healthy, infected or stored milk. The inhibitory effect was reversible on adding 0.75 mm CaCl2, suggesting that chelation of Ca by fraction E was involved in the inhibitory mechanism. However, only partial recovery was achieved and an excess of Ca was required, suggesting the involvement of additional pathways in the process.